Biology subjects

Luo, J.

Publications and source records attributed to Luo, J..

At least 199 records · Page 11Linked to original sources

bioRxiv2023

Proteostasis and lysosomal quality control deficits in Alzheimer's disease neurons

Aging is the most prominent risk factor for Alzheimers disease (AD). However, the cellular mechanisms linking neuronal proteostasis decline to the characteristic aberrant protein deposits in AD brains remain elusive. Here, we develop transdifferentiated neurons (tNeurons) from human dermal fibroblasts as a neuronal model that retains aging hallmarks and exhibits AD-linked vulnerabilities. Remarkably, AD tNeurons accumulate proteotoxic deposits, including phospho-Tau and A{beta}, resembling those in AD patient and APP mouse brains. Quantitative tNeuron proteomics identify aging and AD-linked deficits in proteostasis and organelle homeostasis, most notably in endosome-lysosomal components. Lysosomal deficits in aged tNeurons, including constitutive lysosomal damage and ESCRT-mediated lysosomal repair defects, are exacerbated in AD tNeurons and linked to inflammatory cytokine secretion and cell death. Supporting lysosomal deficits centrality in AD, compounds ameliorating lysosomal function reduce A{beta} deposits and cytokine secretion. Thus, the tNeuron model system reveals impaired lysosomal homeostasis as an early event of aging and AD.

cell biology↗

bioRxiv2023

Variation of wine preference amongst consumers is influenced by the composition of salivary proteins

The preferences of consumers for different flavours and aromas in wine are varied and may be explained by inherent factors such as cultural background, wine education and personal taste of the wine consumer. Wine flavour as perceived in the mouth includes aroma compounds released through the retronasal pathway which are shaped by interactions with saliva. Saliva and wine interactions could provide an explanation as to why wine tasters express different preferences for wine. To test this hypothesis, 13 Western and 13 Chinese experienced wine tasters were recruited. Sensory evaluation was performed in formal surroundings to acquire free description-based and perceived sensory intensity data using the Pivot(R) Profile and continuous scale assessment, respectively. Participants saliva samples were collected before the sensory evaluation and spiked into a wine sample to investigate the impact on the wine volatile release using GCxGC-MS. Saliva samples were subjected to enzyme activity assays and protein composition profiling by Tandem Mass Tag (TMT) quantitative proteomics. The wine tasters showed differences in wine flavour perception, which was supported by the difference in wine volatile release resulting from the addition of saliva. The two groups of participants did not have significant differences in total salivary protein concentrations or the amounts of esterase and -amylase. However, statistically significant variations in the concentrations of specific proteins (proline-rich proteins (PRPs) and lipocalin-1 (LCN-1); p < 0.01) were found between the two groups. Significant correlations between perceived intensities of wine attributes and concentrations of PRPs and LCN-1 were observed. These results indicate that the composition of proteins in saliva are a factor that influences wine perception and preference. Our results provide a biochemical basis to understanding preference for food based on interactions between aroma compounds and salivary proteins and could be used to suggest foods or beverages to particular cultural groups.

biochemistry↗

bioRxiv2023

Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells

The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Genetic mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen (HLA) molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.

genomics↗

bioRxiv2023

Whole mouse body histology using standard IgG antibodies

Most diseases involve multiple interconnected physiological systems, but histological evaluation of their pathology is currently limited to small tissue samples. Here, we present wildDISCO, a technology that uses cholesterol extraction to enable deep tissue penetration of standard 150 kDa IgG antibodies in chemically fixed whole mice. Combining wildDISCO with whole mouse clearing, we generate whole-body maps of the nervous, immune, and lymphatic systems and show their close interactions throughout the mouse body. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/528921v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@f0de23org.highwire.dtl.DTLVardef@187fe94org.highwire.dtl.DTLVardef@15ac0faorg.highwire.dtl.DTLVardef@133703e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIWildDISCO uses new tissue chemistry based on {beta}-cyclodextrin to enable histology in whole mouse bodies using full-size antibodies C_LIO_LIWildDISCO generates the first whole mouse body atlases for neurons, immune cells, blood and lymph vessels C_LIO_LIThe whole mouse atlases are available online to study the biological systems in health and disease C_LIO_LIVirtual Reality (VR) exploration of these atlases disentangles complex anatomical structures between organs and biological systems C_LI Supplementary Videos can be seen athttp://discotechnologies.org/wildDISCO/

biochemistry↗

bioRxiv2023

Two teosintes made modern maize

Despite its global importance as a crop with broad economic, dietary, and cultural importance, the origins of maize and its closest wild relatives remained the topic of vigorous debate for nearly a century. Molecular analyses ultimately concluded that maize was domesticated once from a common ancestor with its closest extant relative, the lowland wild grass Zea mays ssp. parviglumis. But neither the current genetic model nor earlier models based on archaeological data account for the totality of available data, and recent work has highlighted the potential contribution of a second wild relative, the highland Zea mays ssp. mexicana. Here we present a detailed population genetic analysis of the contributions of both wild taxa to modern maize diversity using the largest sample of traditional maize varieties sequenced to date. We show that all modern maize can trace its origin to an ancient admixture event between domesticated ancient maize and Zea mays ssp. mexicana in the highlands of Mexico ca 5300 cal BP, some 4,000 years after domestication began. We show that variation in admixture is a key component of modern maize genetic and phenotypic diversity, both at the level of individual loci and as a factor driving a substantial component of additive genetic variation across a number of agronomic traits. Our results clarify the long-debated origin of modern maize, highlight the potential contributions of crop wild relatives to agronomic improvement, and raise new questions about the anthropogenic mechanisms underlying multiple waves of dispersal throughout the Americas. One-Sentence SummaryOur results clarify the long-debated origin of modern maize and highlight the contributions of crop wild relatives to the agronomic improvement of modern varieties.

evolutionary biology↗

bioRxiv2023

Quantitative Annotations of T-Cell Repertoire Specificity

The specificity of a T-cell receptor (TCR) repertoire determines personalized immune capacity. Existing methods have modelled the qualitative aspects of TCR specificity, while the quantitative aspects remained unaddressed. We developed a package, TCRanno, to quantify the specificity of TCR repertoires. Applying TCRanno to 4,195 TCR repertoires revealed quantitative changes in repertoire specificity upon infections, autoimmunity and cancers. Specifically, TCRanno found cytomegalovirus-specific TCRs in seronegative healthy individuals, supporting the possibility of abortive infections. TCRanno discovered age-accumulated fraction of SARS-CoV2-specific TCRs in pre-pandemic samples, which may explain the aggressive symptoms and age-related severity of COVID-19. TCRanno also identified the encounter of Hepatitis B antigens as a potential trigger of systemic lupus erythematosus. TCRanno annotations showed capability in distinguishing TCR repertoires of healthy and cancers including melanoma, lung and breast cancers. TCRanno may also facilitate single-cell TCRseq+gene expression data analyses by isolating T-cells with the specificity of interest.

bioinformatics↗

bioRxiv2023

Analysis of Biodeterioration on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing and Conventional Culturing Methods

AbstractWooden buildings are facing biodeterioration due to natural weathering. Ancestral halls are traditional Chinese wooden architecture with high artistic value. The research analyzed the microbial diversity of nine ancestral halls in Guangdong Province under subtropical monsoon climates. With amplicon sequencing, we found a common core microorganism group, including Bacillus, Pseudomonas, Paenibacillus, Acinetobacter, Toxicocladosporium, Cladosporium, Aspergillus, and Epicoccum. A total of 8 different species of bacteria and 7 different species of fungi were isolated from Chen Clan Ancestral halls, most of which were proven to be capable of degrading cellulose or lignin. The comparison between damaged and undamaged sites (whether the paint coating is flaked off) revealed similar microbial compositions but with differing abundances. Firmicutes and Ascomycota dominated damaged surfaces, while Proteobacteria and Actinobacteria prevailed in undamaged ones. Notably, Cladosporium, widely present in both sites, emerged as the primary cellulose-degrading genus. Given the similar microbial compositions between damaged and undamaged sites, it is suggested that using paint alone as the exclusive means to protect bare wood is insufficient. Apparent correlation between microorganisms on wooden surfaces and humans showed that the increase of visitor flow rates might impact the microbiota composition on cultural relics. We evaluated the effect of four representative biocides and determined the feasibility of low-concentration Isothiazolinone. This research facilitates a basic understanding of the microbial weathering of ancestral halls and add significant reference for preserving wooden structures.

microbiology↗

bioRxiv2022

A non-conserved histidine residue on KRAS drives paralog selectivity of the KRAS G12D inhibitor MRTX1133

The discovery of small molecule inhibitors against mutant KRAS protein was a recent breakthrough in targeted therapy. Understanding the mechanism of selectivity by KRAS inhibitors and the mechanism of resistance to them can guide the future development of KRAS inhibitors. MRTX1133 was the first non-covalent inhibitor against the KRAS G12D mutant that demonstrated specificity and potency in pre-clinical tumor models. We used isogenic cell lines expressing a single RAS allele to evaluate the selectivity of this compound. We found that in addition to KRAS G12D, MRTX1133 shows significant activity against several other KRAS mutants as well as wildtype KRAS protein. In contrast, MRTX1133 exhibits no activity against both G12D and wildtype forms of HRAS and NRAS proteins. Functional analysis revealed that the selectivity of MRTX1133 towards KRAS is associated with its binding to histidine 95 on KRAS, a residue that is not conserved in HRAS and NRAS. Reciprocal mutation of amino acid 95 among the three RAS paralogs resulted in reciprocal change in their sensitivity towards MRTX1133. Thus, histidine 95 is an essential selectivity handle for MRTX1133 towards KRAS. This knowledge could aid the development of future KRAS-selective inhibitors.

cancer biology↗

bioRxiv2022

Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes

Dynamic conformational and structural changes in proteins and protein complexes play a central and ubiquitous role in the regulation of protein function, yet it is very challenging to study these changes, especially for large protein complexes, under physiological conditions. Here we introduce a novel isobaric crosslinker, Qlinker, for studying conformational and structural changes in proteins and protein complexes using quantitative crosslinking mass spectrometry (qCLMS). Qlinkers are small and simple, amine-reactive molecules with an optimal extended distance of [~]10 [A] which use MS2 reporter ions for relative quantification of Qlinker-modified peptides derived from different samples. We synthesized the 2-plex Q2linker and showed that the Q2linker can provide quantitative crosslinking data that pinpoints key conformational and structural changes in biosensors, binary and ternary complexes composed of the general transcription factors TBP, TFIIA, and TFIIB, and RNA polymerase II (pol II) complexes.

systems biology↗

bioRxiv2022

Contrastive learning of protein representations with graph neural networks for structural and functional annotations

Although protein sequence data is growing at an ever-increasing rate, the protein universe is still sparsely annotated with functional and structural annotations. Computational approaches have become efficient solutions to infer annotations for unlabeled proteins by transferring knowledge from proteins with experimental annotations. Despite the increasing availability of protein structure data and the high coverage of high-quality predicted structures, e.g., by AlphaFold, many existing computational tools still only rely on sequence data to predict structural or functional annotations, including alignment algorithms such as BLAST and several sequence-based deep learning models. Here, we develop PenLight, a general deep learning framework for protein structural and functional annotations. PenLight uses a graph neural network (GNN) to integrate 3D protein structure data and protein language model representations. In addition, PenLight applies a contrastive learning strategy to train the GNN for learning protein representations that reflect similarities beyond sequence identity, such as semantic similarities in the function or structure space. We benchmarked PenLight on a structural classification task and a functional annotation task, where PenLight achieved higher prediction accuracy and coverage than state-of-the-art methods.

bioinformatics↗

bioRxiv2022

Antagonistic roles of canonical and alternative RPA in tandem CAG repeat diseases

Tandem CAG repeat expansion mutations cause >15 neurodegenerative diseases, where ongoing expansions in patients brains are thought to drive disease onset and progression. Repeat length mutations will involve single-stranded DNAs prone to form mutagenic DNA structures. However, the involvement of single-stranded DNA binding proteins (SSBs) in the prevention or formation of repeat instability is poorly understood. Here, we assessed the role of two SSBs, canonical RPA (RPA1-RPA2-RPA3) and the related Alternative-RPA (Alt-RPA, RPA1-RPA4-RPA3), where the primate-specific RPA4 replaces RPA2. RPA is essential for all forms of DNA metabolism, while Alt-RPA has undefined functions. RPA and Alt-RPA are upregulated 2- and 10-fold, respectively, in brains of Huntington disease (HD) and spinocerebellar ataxia type 1 (SCA1) patients. Correct repair of slipped-CAG DNA structures, intermediates of expansion mutations, is enhanced by RPA, but blocked by Alt-RPA. Slipped-DNAs are bound and melted more efficiently by RPA than by Alt-RPA. Removal of excess slipped-DNAs by FAN1 nuclease is enhanced by RPA, but blocked by Alt-RPA. Protein-protein interactomes (BioID) reveal unique and shared partners of RPA and Alt-RPA, including proteins involved in CAG instability and known modifiers of HD and SCA1 disease. RPA overexpression inhibits rampant CAG expansions in SCA1 mouse brains, coinciding with improved neuron morphology and rescued motor phenotypes. Thus, SSBs are involved in repeat length mutations, where Alt-RPA antagonistically blocks RPA from suppressing CAG expansions and hence pathogenesis. The processing of repeat length mutations is one example by which an Alt-RPA{leftrightarrow}RPA antagonistic interaction can affect outcomes, illuminating questions as to which of the many processes mediated by canonical RPA may also be modulated by Alt-RPA.

genetics↗

bioRxiv2022

Mating strategies in Caenorhabditis elegans populations are determined by male developmental history

Mating strategies, whether sexual or asexual, confer unique costs and benefits to populations and species that facilitate evolutionary processes. In wild isolates of Caenorhabditis elegans, mating strategies are dependent on developmental history. Outcrossing levels significantly increase when one or both parents have transiently passed through the stress-resistant dauer diapause stage. However, the molecular mechanisms of how life history alters mating strategies have not been systematically explored. Sex-specific responses to pheromones are a major driver of mating behaviors in C. elegans. We demonstrated previously that postdauer hermaphrodites exhibit a decreased avoidance of the pheromone ascr#3 due to the downregulation of the osm-9 TRPV channel gene in postdauer ADL neurons. Thus, we hypothesized that altered responses to pheromones in postdauer animals could contribute to increased outcrossing. We conducted mating assays using wild type N2 Bristol, as well as daf-3/co-SMAD and mut-16/Mutator strains that fail to downregulate osm-9 in postdauer hermaphrodite ADL neurons. First, we show that the outcrossing level of N2 Bristol correlated with the developmental history of males, and that postdauer males exhibited an increased ability to detect mates via pheromones compared to continuously developed males. In addition, DAF-3 plays a critical role in postdauer males to regulate mating, while playing a more minor role in hermaphrodites. Furthermore, the mut-16 strain exhibited negligible outcrossing, and attempts to rescue the outcrossing phenotype resulted in transgenerational sterility due to germline defects. Together, our results suggest a model whereby mating strategy is driven by developmental history under combinatorial control of TGF-{beta} and RNAi pathways.

genetics↗

bioRxiv2022

DEED: A Dataset for Dream-related Emotion Research

Emotion is closely related to human cognition and behaviour. In recent years, scholars have conducted extensive research on emotion in waking state based on electroencephalography (EEG) and achieved certain results. However, Emotional activity continues after sleep, with a concentrated response of sleep emotions in dreams. Sleep emotions are concentrated in dreams, which can better reflect a series of real physical and psychological states of the human body. Currently, there is no publicly available dataset for the assessment of dream mood. Therefore, we present a physiological dataset Dream Emotion Evaluation Dataset (DEED) for the assessment of dream mood, which recorded EEG signals from 38 participants over 89 whole sleep nights and 533 dream segments(after exclusion of unqualified nights, those dream segments are extracted from 82 whole sleep nights). We studied the correlations between the subjective ratings and the EEG signals and brain network patterns for dream emotions. In addition, the relationship between the asymmetry of left and right brain bands and positive and negative dream emotions was studied. The machine learning algorithm was also used to classify different emotional EEG, which confirmed the validity of the dataset. In the meantime, we encourage other researchers to explore the underlying neural mechanisms involved in sleep.

neuroscience↗

bioRxiv2022

3rd-ChimeraMiner: A pipeline for integrated analysis of whole genome amplification generated chimeric sequences using long-read sequencing

Multiple displacement amplification (MDA) has become one of the most commonly used method of whole genome amplification (WGA) due to the high processivity, strand displacement capacity and high fidelity of the phi29 DNA polymerase, MDA generate vast amount of DNA with higher molecules weight (up to 100kb) and greater genome coverage. Along with the development of the sequencing platform, it is possible to sequence the MDA-amplified DNA molecules with over 20kb by long-read sequencing. However, one of the challenges is the formation of chimeras, which exist in all MDA products, and seriously interfere with the downstream analysis of the long-read sequencing data of MDA-amplified DNA. In this study, we constructed 3rd-ChimeraMiner, a chimera detection pipeline for analyzing the long-read sequencing of MDA products, recognizing chimeras, and integrating chimeras into the downstream analysis. Five sequencing data of MDA with different magnification fold were analyzed in here, the proportions of chimeras are much higher than that of next-generation sequencing reads and increase with the increase of magnification folds, ranging from 42% to over 76%. After comparing, 99.92% of recognized chimeras have been demonstrated not to exist in original genomes. After detecting chimeras by 3rd-ChimeraMiner, the full-length mapping ratio increased, means more PacBio data could be used in downstream analysis, and mean 97.77% inversions were removed after transferred chimeras into normal reads. 3rd-ChimeraMiner revealed efficiency and accuracy in discovering chimeras from long-read sequencing data of MDA, and is promising to be widely used in single-cell sequencing.

bioinformatics↗

bioRxiv2022

The Chromosome-based Genome of Paspalum vaginatum Provides New Insights into Salt-stress Adaptation

Salinization is increasingly a major factor limiting production worldwide. Revealing the mechanism of salt tolerance could help to create salt-tolerant crops and improve their yields. We reported a chromosome-scale genome sequence of the halophyte turfgrass Paspalum vaginatum, and provided structural evidence that it shared a common ancestor with Z. mays and S. bicolor. A total of 107 P. vaginatum germplasms were divided into two groups (China and foreign group) based on the re-sequenced data, and the grouping findings were consistent with the geographical origin. Genome-wide association study (GWAS) of visually scored wilting degree and withering rates identified highly significant QTL on chromosome 6. Combination with RNA-seq, we identified a significantly up-regulated gene under salt stress, which encodes High-affinity K+ Transporter 7 (PvHKT7), as strong candidates underlying the QTL. Overexpression of this gene in Arabidopsis thaliana significantly enhanced salt tolerance by increasing K+ absorption. This study adds new insights into salt-stress adaptation of P. vaginatum and serve as a resource for salt-tolerant improvement of grain crops.

genomics↗

bioRxiv2022

The porcine cGAS-STING pathway exerts an unusual antiviral function independent of IFN and autophagy

The innate immune DNA sensing cGAS-STING pathway exerts strong antiviral activity through the downstream interferon (IFN) production; however, it has been recently recognized that IFN independent activity of STING also plays an important role in antiviral functions. Nevertheless, the IFN independent antiviral activity of STING is not fully understood. In this study, we showed that porcine STING (pSTING) played a critical role in anti-HSV1 and anti-VSV infections, and IFN defective mutants including pSTING pLxIS sub, S365A and {Delta}CTT all exhibited similar antiviral functions to wild type (WT) pSTING. Further, all these IFN defective pSTING mutants possessed a comparable autophagy activity relative to WT pSTING as expected. From pSTING WT, S365A and {Delta}CTT, the residues responsible for autophagy were mutated, which included L333A/R334A, Y167A/L170A and Y245A/L248A, respectively. Surprisingly, all these autophagy defective pSTING mutants still resisted from the two viral infections, demonstrating the pSTING antiviral function independent of IFN as well as autophagy. On the other hand, all the autophagy defective pSTING mutants triggered cell apoptosis, which was associated with the antiviral functions. Additionally, pSTING lost its antiviral activity in TBK1-/- and IRF3-/- porcine macrophages, indicating the involvement of TBK1 and IRF3 in other STING activity such as apoptosis. Collectively, our results revealed that STING exerts both IFN and autophagy independent antiviral activity, and also suggested that STING triggered cell apoptosis might resist from virus infections.

immunology↗

bioRxiv2022

Multimodal electrocorticogram active electrode array based on zinc oxide-thin film transistors

Active electrocorticogram (ECoG) electrodes can amplify the weak electrophysiological signals and improve the anti-interference ability, but the traditional active electrodes are so opaque that cannot realize photoelectric collaborative observation. Here an active and fully-transparent ECoG array based on zinc oxide-thin film transistors (ZnO-TFTs) was developed as the local neural signal amplifier for electrophysiological monitoring. The transparency of the proposed ECoG array was up to 85% which is superior to previous reported active electrode array. Various electrical characterizations demonstrated its ability of electrophysiological signal recording, with a higher signal-to-noise ratio of 19.9 dB compared to the Au grid one (13.2 dB). The high transparency of ZnO-TFT electrode array allowed the collecting electrophysiological signals under direct light stimulation on optogenetic mice brain concurrently. The ECoG array could also work under 7-Tesla magnetic resonance imaging to record local brain signal without affecting brain tissue imaging. As the most transparent active ECoG array to date, it provides a powerful multimodal tool for brain observation, including recording brain activity under synchronized optical modulation and 7-Tesla magnetic resonance imaging.

bioengineering↗

bioRxiv2022

Multi-Domain Characterization and Rapid Detection Technology for Cocaine and Methamphetamine Acute Abuse based on EEG

Multi-domain characterization and a new fast detection method for acute illegal psychostimulants abuse detection based on waking-state EEG of mice is proposed in this paper. To get corftical electroencephalogram (EEG), three groups of mice were injected with cocaine (Coca), methamphetamine (Meth), and saline (Sali) respectively following the experimental paradigm of drug abuse. The EEG features were extracted out by multi-domain views, including time, frequency, complexity, dynamics, and independent domains to obtain acute drug abuse effects on the brain. New strategy combing time domain with frequency domain is developed as multi-domain input and by means of dimension transformation approach preserving temporal information, the performance of drug abuse detection is greatly improved with deep learning models of ResNet50. Results show that comparing to support vector machine (SVM), k nearest neighbor (kNN), random forest (RF), and long short-term memory fully convolutional networks (LSTM-FCN), ResNet50 based on our proposed multi-domain features has best F1-score of 95.10%. This promising method provides a low-cost, fast, and widely assisted technology for psychostimulants abuse identification.

bioinformatics↗